The Bury side contained seven players who had appeared at first team level but were beaten by goals from Stephen Ireland (41), Karl Bermingham (47) and Micah Richards (88).
Lee Croft set up Ireland for the opener before Bury keeper cleared a chance from Croft but only as far as Bermingham, who lobbed the stranded keeper from 25 yards.
Substitute Richards combined with Bermingham, and the England U17 ace scored his debut goal at reserve level.
Bury striker Colin Kazim Richards almost equalised before the break but struck the woodwork.
City: Ellegaard; Lee-Matthews, Williamson, J D’Laryea, N D’Laryea, Collins, Croft (Grimes 74), Ireland (Richards 74), Bermingham, Bennett, Tandy (Laird 77). Subs: Schmeichel (GK), Warrender.